REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antbodies
Ant-mouse CD4 (GK1.5) APC	Biolegend	Cat#: 100412; RRID: AB_312697
Ant-mouse CD4 (GK1.5) PerCP-Cy5.5	Biolegend	Cat#: 100432; RRID: AB_893323
Ant-mouse IL-17A (TC11–18H10.1) PE	Biolegend	Cat#: 506904; RRID: AB_315464
Ant-mouse IFNγ (XMG1.2) PE-Cy7	Biolegend	Cat#: 505826; RRID: AB_2295770
Ant-mouse IL-10 (JESE-16E3) BrilliantViolet421	Biolegend	Cat#: 505022; RRID: AB_3563240
Ant-mouse RORγt (Q31–378) PerCP-Cy5.5	BD Biosciences	Cat#: 562683; RRID: AB_2737720
Ant-mouse FoxP3 (FJK-16 s) PE	eBioscience	Cat#: 12–5773-80; RRID: AB_465935
Ant-mouse GATA3 (16E10A23) BrilliantViolet421	BD Biosciences	Cat#: 560405; RRID: AB_1645544
Ant-mouse CD45RB (C363–16A) FITC	Biolegend	Cat#: 103306; RRID: AB_313013
Ant-mouse CD25(PC61) PE	Biolegend	Cat#: 102008; RRID: AB_312857
Ant-mouse Helios (22F6) FITC	Biolegend	Cat#: 137214; RRID: AB_10662745
Ant-mouse I-A/I-E (M5/114.15.2) Pacific Blue	Biolegend	Cat#: 107620; RRID: AB_493527
Ant-mouse CD11c (N418) PE-Cy7	Biolegend	Cat#: 117318; RRID: AB_493568
Ant-mouse CD11b (M1/70) PerCP-Cy5.5	Biolegend	Cat#: 101230; RRID: AB_2129374
Ant-mouse CD64 (X54–5/7.1) PE	Biolegend	Cat#: 139304; RRID: AB_10612740
Ant-mouse CD86(GL-1) FITC	Biolegend	Cat#: 105006; RRID: AB_313149
Ant-mouse CD80 (16–10A1) APC	Biolegend	Cat#: 104714; RRID: AB_313135
Ant-mouse CD3 (17A2) BrilliantViolet421	Biolegend	Cat#: 100228; RRID: AB_2562553
Ant-mouse CD19 (6D5) BrilliantViolet421	Biolegend	Cat#: 115538; RRID: AB_11203527
Ant-mouse IL-22 (Poly5164) PE	Biolegend	Cat#: 366704; RRID: AB_2565568
Ant-mouse IL-17A (TC11–18H10.1) PE-Cy7	Biolegend	Cat#: 506922; RRID: AB_2125010
Ant-mouse NKp46 (29A1.4) APC	Biolegend	Cat#: 137608; RRID: AB_10612758
Ant-mouse Csf2 (MP1–22E9) FITC	Biolegend	Cat#: 505404; RRID: AB_315380
Biological Samples
32 human stool samples	Jacobs et.al. 2016 and this study	N/A
17 arrayed culture collections of human microbiotas	This study	N/A
Chemicals, Peptides, and Recombinant Proteins
DNase 1	Sigma Aldrich	Cat#: DN25
Collagenase	Sigma Aldrich	Cat#: C5138
EDTA	Ambion	Cat# AM9260G
HEPES	Caisson	Cat#: HOL06
Fetal bovine serum	Thermo Fisher Scientific	Cat#: 10438026
ACK Lysis Buffer	GIBCO	Cat#: A1049201
Zombie Aqua Fixable Viability Dye	Biolegend	Cat#: 423102
Phorbal 12-myristate 13-acetate	Sigma Aldrich	Cat#: P8139
lonomycin	Sigma Aldrich	Cat#: I3909
Monensin	Biolegend	Cat#: 420701
Brefeldin A	Biolegend	Cat#: 420601
Critical Commercial Assays
Mouse Lipocalin-2/NGAL Duoset ELISA	R&D Systems	Cat#: DY1857
FoxP3/Transcription Factor Staining Buffer Set	Thermo Fisher Scientific	Cat#: 00–5523-00
Intracellular Fixation and Permeabilization Buffer Set	Thermo Fisher Scientific	Cat#: 88–8824-00
MagniSort Mouse CD4 T cell Enrichment Kit	Thermo Fisher Scientific	Cat#: 8804–6821-74
QIAquick 96 PCR Purification Kit	QIAGEN	Cat# 28181
Quant-IT dsDNA Assay Kit - High Sensitivity	Thermo Fisher Scientific	Cat# Q33130
Quant-IT dsDNA Assay Kit - Broad Range	Thermo Fisher Scientific	Cat# Q32853
Deposited Data
16S rDNA amplicon sequencing	Contijoch et al. (2018) and this manuscript	NCBI: PRJNA436992
16S rDNA amplicon sequencing	Contijoch et al. (2018) and this manuscript	NCBI: PRJNA413199
Greengenes reference database version 13_8	DeSantis et al., 2006	http://greengenes.lbl.gov
Experimental Models: Organisms/Strains
Germ free C57BL/6J	Mount Sinai Gnotobiotic Facility	N/A
Germ free B6.129S7-Rag1tm1Mom/J	Mount Sinai Gnotobiotic Facility	N/A
Specific Pathogen Free C57BL/6J	Jackson Labs	MGI:5657312
Specific Pathogen Free C57BL/6NTac	Taconic Farms	MGI:5658006
Oligonucleotides
16S V4 (515–806) F 5’-GTGCCAGCAGCCGCGGTAA-3’	IDT (Relman et al., 1992)	N/A
16S V4 (515–806) R 5’-GGACTACCAGGGTATCTAAT-3’	IDT (Relman et al., 1992)	N/A
Software and Algorithms
R Studio	R Studio	N/A
FlowJo X	Tree Star	N/A
MacQIIME	Caporaso et al., 2010	N/A
FACSDiva	BD Biosciences	N/A
Phyloseq	McMurdie and Holmes, 2013	N/A
Prism 6	GraphPad	N/A